It's no secret that Greek yogurt's popularity is on the rise and consumers are increasingly losing their appetite for cereal. But recent data show the trends are picking up speed and creating major headaches for some of the companies behind America's best-known breakfast brands.

General Mills on Wednesday reported sales that came short of analysts' estimates, in part due to consumers' changing breakfast habits.

Here are three ways Americans are fundamentally taking a different approach to their first meal of the day, and who may be the winners and losers in the shift in breakfast habits.

Cereal declines

Cereal sales and volumes have been steadily declining for more than a year, with sales falling 7 percent in the latest four-week period, according to Nielsen ScanTrack data.

Kellogg, which relies on cereal for about 30 percent of its total sales, got hit the hardest, with cereal sales down 10 percent for the period. It was followed by private label General Mills, which gets about 20 percent of its sales from cereal; Post, which puts out cereals such as Grape-Nuts and Fruity Pebbles; and PepsiCo, which owns Quaker.

To combat the decline, brands are introducing new products and trying to get the message out that cereal is healthy.

Kellogg, which most recently cited weakness in its Special K, Frosted Mini-Wheats and Kashi brands, is working to improve consumers' perceptions by what it calls "health-related messaging." It's trying to remind consumers that cereals can be a source of protein, which is popular right now and among the reasons yogurt and meat sales have surged.

Sofie Delauw | Cultura | Getty Images

As Kellogg CEO John Bryant noted on the first-quarter conference call in May, the company is finding that consumers don't realize that in "a bowl of Mini-Wheats and milk, there's as much protein as in many yogurts."

He called it an "opportunity to reappraise and reconsider cereal and milk" for breakfast consumers.

Kellogg is also trying to pivot to healthier, buzzier products such as non-GMO verified Kashi and new cereal snacks that capitalize on the growing snacking trend. Bryant said he expects cereal consumption to continue to decline, but at a more moderate rate, for the rest of the year.

General Mills has also invested in advertising campaigns to raise awareness about the nutritional benefits of cereal and is emphasizing its Yoplait yogurt portfolio that includes Yoplait Greek. The company raised expectations on Wednesday citing product upgrades, including more cinnamon taste in Cinnamon Toast Crunch and fruitier tasting Trix.

It's also bringing more protein to its other popular franchises—Cheerios and Nature Valley.

"Consumers today are seeking more protein at breakfast and we're responding," CEO Kendall J. Powell said in the company's earnings call.

Yogurt explosion

With cereal on the decline, yogurt consumption has surged.

It's a $4.2 billion industry, according to IBISWorld, with nearly a third made up of Greek-style yogurt.

"The growth in establishments can be attributed to the increasing popularity of Greek-style yogurt and the rising per capita consumption of yogurts products in general," according a September report from the research firm. "Even during the height of the recession, consumption of yogurt products rose 5.5 percent in 2009, according to the USDA."

Consumer Edge Research looked at breakfast consumption from 2003 to 2013 and found that adults regularly starting the day with yogurt jumped to 49 percent, from 36 percent.The gains are spread across all age groups, from 18-year-olds to those 65 and older.

Bill Pecoriello, CEO of Consumer Edge Research, said it's the private companies such as Chobani that are growing the fastest. Earlier this month the yogurt maker said that it will launch its largest portfolio expansion in history.

Eating breakfast out

The other major breakfast trend businesses can't afford ignore: Americans are increasingly eating the meal out of the house. It's no wonder Taco Bell, Burger King, Starbucks, andDunkin' Donuts are launching breakfast burgers, waffle tacos and more to compete with McDonald's dominant hold on the market.

The reason: Although it still makes up a small percentage of total sales, it's the only part of the day that's seeing traffic growth. Guest Metrics data shows that of the five parts of the day (breakfast, lunch, happy hour, dinner and late night), breakfast was the only one with positive traffic through May.

The most popular items are sandwiches, breakfast burritos and yogurts, while scones, doughnuts and muffins are not as hot, Pecoriello said.

According to RBC's food industry analyst Dave Palmer, Starbucks is in the best position to capture sales from the various shifts in consumer habits around breakfast.

But organic, health-focused brands such as WhiteWave, which makes Silk dairy alternatives, and Hain Celestial, which is behind Greek Gods Yogurt, are also in strong positions.

Still, the ultimate winners may be the companies facing challenges. That's because analysts say the sector is ripe for consolidation, with deal speculation recently centering on General Mills and Kellogg.

But whether its deals, new innovative products or increased marketing spending, the bottom line is that food companies are scrambling to catch up with changes in the way we eat after waking up.

—By CNBC's Sara Eisen

Sara Eisen"Squawk on the Street" Co-Anchor and "Worldwide Exchange" Co-Anchor